ArticleJournal of bacteriology2003
Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis.
Article in Journal of bacteriology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Laboratory Diagnosis of Human Brucellosis.Clinical microbiology reviews · 2019Review
- RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection.PLoS pathogens · 2018Article
- Long-range dispersal movedMicrobial genomics · 2016Article
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- Using biological networks to improve our understanding of infectious diseases.Computational and structural biotechnology journal · 2014Review
- Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates.BMC genomics · 2014Article
- Cough aerosols of Mycobacterium tuberculosis predict new infection: a household contact study.American journal of respiratory and critical care medicine · 2013Article
- Global analysis of mRNA stability in Mycobacterium tuberculosis.Nucleic acids research · 2013Article
- Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database.Tuberculosis (Edinburgh, Scotland) · 2013Review
- Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance.Antimicrobial agents and chemotherapy · 2012Review
- Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains).Microbial informatics and experimentation · 2012Article
- Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles.BMC microbiology · 2012Article
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- Article
- SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes.PloS one · 2011Article
- Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival.PLoS pathogens · 2010Article
- Bacterial genetic signatures of human social phenomena among M. tuberculosis from an Aboriginal Canadian population.Molecular biology and evolution · 2010Article
- Landscape epidemiology of tularemia outbreaks in Sweden.Emerging infectious diseases · 2009Article
- Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.BMC biology · 2009Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared "reference strains." Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI "C" strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.